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Updated: May 26, 2026

Multi-locus Variable-number Tandem-repeat Analysis of the Fish-pathogenic Bacterium Yersinia ruckeri by Multiplex PCR and Capillary Electrophoresis

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High-resolution melting genotyping of Enterococcus faecium based on multilocus sequence typing derived single

Steven Y C Tong¹, Shirley Xie, Leisha J Richardson

¹Menzies School of Health Research, Darwin, Northern Territory, Australia. Steven.tong@menzies.edu.au

|December 24, 2011

Summary

A new high-resolution melting (HRM) genotyping technique accurately identifies Enterococcus faecium strains. This rapid, reproducible method offers improved resolution compared to existing SNP typing, aligning well with multilocus sequence typing (MLST) and PFGE.

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Methods to Increase the Sensitivity of High Resolution Melting Single Nucleotide Polymorphism Genotyping in Malaria

Methods to Increase the Sensitivity of High Resolution Melting Single Nucleotide Polymorphism Genotyping in Malaria

Published on: November 10, 2015

Area of Science:

Microbiology
Molecular Biology
Genetics

Background:

Enterococcus faecium is a significant opportunistic pathogen, often associated with hospital-acquired infections.
Accurate and rapid genotyping methods are crucial for tracking E. faecium outbreaks and understanding its population structure.
Existing methods like MLST and PFGE are valuable but can be time-consuming or require specialized equipment.

Purpose of the Study:

To develop and validate a novel single nucleotide polymorphism (SNP) nucleated high-resolution melting (HRM) technique for genotyping Enterococcus faecium.
To assess the discriminatory power and concordance of the HRM method compared to established genotyping techniques.
To evaluate the utility of HRM for E. faecium population structure analysis.

Main Methods:

Eight SNPs from the E. faecium MLST database were selected.
Fragments containing these SNPs were amplified and analyzed using HRM.
The HRM genotyping scheme was tested on 85 E. faecium bloodstream isolates.
Results were compared with MLST, PFGE, and allele-specific real-time PCR (AS kinetic PCR) SNP typing.

Main Results:

The HRM method resolved E. faecium into 231 distinct "melting types" (MelTs), achieving a high Simpson's Index of Diversity (D) of 0.991.
This represents a significant improvement in discriminatory power compared to AS kinetic PCR (61 SNP types, D=0.95).
Excellent concordance was observed between HRM, MLST, and PFGE (Adjusted Rand Indices of 0.973 and 0.936, respectively).

Conclusions:

The developed SNP-nucleated HRM technique is a rapid, reproducible, and highly discriminatory method for genotyping Enterococcus faecium.
HRM provides results concordant with MLST, enabling effective population structure analysis.
This method offers a valuable alternative for routine E. faecium surveillance and outbreak investigation.